Mercurial > repos > lparsons > cutadapt
annotate macros.xml @ 3:d0e40ca0cad6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
| author | iuc |
|---|---|
| date | Thu, 24 May 2018 18:23:52 -0400 |
| parents | a018169c73d2 |
| children | b58d26072ded |
| rev | line source |
|---|---|
|
2
a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
1 <macros> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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2 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
3 <token name="@read1_options@"><![CDATA[ |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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4 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
5 ## Read1 trimming |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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6 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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7 #for $a in $library.r1.adapters |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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8 #if $a.adapter_source.adapter_source_list == 'builtin': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
9 -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
10 #else if str($a.adapter_source.adapter_name) != "": |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
11 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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12 #else |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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13 -a '${a.adapter_source.adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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14 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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15 #end for |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
16 #for $aa in $library.r1.anywhere_adapters |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
17 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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18 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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19 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
20 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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21 #else |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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22 -b '${aa.anywhere_adapter_source.anywhere_adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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23 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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24 #end for |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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25 #for $fa in $library.r1.front_adapters |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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26 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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27 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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28 #else if str($fa.front_adapter_source.front_adapter_name) != "": |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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29 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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30 #else |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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31 -g '${fa.front_adapter_source.front_adapter}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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32 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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33 #end for |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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34 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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35 #if str($library.r1.cut) != '0': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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36 -u $library.r1.cut |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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37 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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38 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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39 ## Additional Outputs |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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40 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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41 #if $output_options.info_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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42 --info-file=$info_file |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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43 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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44 #if $output_options.rest_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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45 --rest-file=$rest_output |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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46 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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47 #if $output_options.wildcard_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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48 --wildcard-file=$wild_output |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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49 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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50 #if $output_options.too_short_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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51 --too-short-output=$too_short_output |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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52 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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53 #if $output_options.too_long_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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54 --too-long-output=$too_long_output |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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55 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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56 #if $output_options.untrimmed_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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57 --untrimmed-output=$untrimmed_output |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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58 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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59 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
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60 ]]></token> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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61 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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62 <token name="@read2_options@"><![CDATA[ |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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63 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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64 ## Read2 trimming |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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65 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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66 #for $a in $library.r2.adapters2 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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67 #if $a.adapter_source2.adapter_source_list2 == 'builtin': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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68 -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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69 #else if str($a.adapter_source2.adapter_name2) != "": |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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70 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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71 #else |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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72 -A '${a.adapter_source2.adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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73 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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74 #end for |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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75 #for $aa in $library.r2.anywhere_adapters2 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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76 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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77 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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78 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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79 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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80 #else |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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81 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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82 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
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changeset
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83 #end for |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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84 #for $fa in $library.r2.front_adapters2 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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85 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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86 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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87 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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88 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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89 #else |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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90 -G '${fa.front_adapter_source2.front_adapter2}' |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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91 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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92 #end for |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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93 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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94 #if str($library.r2.cut2) != '0': |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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95 -U $library.r2.cut2 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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96 #end if |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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97 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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98 ## Additional Outputs - Read 2 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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99 |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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100 #if $output_options.too_short_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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101 --too-short-paired-output=$too_short_paired_output |
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a018169c73d2
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102 #end if |
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a018169c73d2
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103 #if $output_options.too_long_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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104 --too-long-paired-output=$too_long_paired_output |
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a018169c73d2
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105 #end if |
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a018169c73d2
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106 #if $output_options.untrimmed_file: |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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107 --untrimmed-paired-output=$untrimmed_paired_output |
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a018169c73d2
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108 #end if |
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a018169c73d2
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109 |
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a018169c73d2
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110 ]]></token> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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111 |
|
a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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112 <xml name="single_end_options" > |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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113 |
|
a018169c73d2
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114 <section name="r1" title="Read 1 Options" expanded="True"> |
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a018169c73d2
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115 |
|
a018169c73d2
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116 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
|
a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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117 <conditional name="adapter_source"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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118 <param name="adapter_source_list" type="select" label="Source" > |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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119 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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120 <option value="user">Enter custom sequence</option> |
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a018169c73d2
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121 </param> |
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a018169c73d2
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iuc
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122 |
|
a018169c73d2
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123 <when value="user"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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124 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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125 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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126 </when> |
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127 |
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128 <when value="builtin"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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129 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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130 <options from_data_table="adapters"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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131 <filter type="sort_by" column="1" /> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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132 </options> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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133 </param> |
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a018169c73d2
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134 </when> |
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a018169c73d2
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135 </conditional> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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136 </repeat> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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137 |
|
a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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138 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
|
a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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139 <conditional name="front_adapter_source"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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140 <param name="front_adapter_source_list" type="select" label="Source"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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141 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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142 <option value="user">Enter custom sequence</option> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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143 </param> |
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a018169c73d2
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144 |
|
a018169c73d2
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145 <when value="user"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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146 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional)" /> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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147 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> |
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a018169c73d2
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148 </when> |
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149 <when value="builtin"> |
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a018169c73d2
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150 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter"> |
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a018169c73d2
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151 <options from_data_table="adapters"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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152 <filter type="sort_by" column="1" /> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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153 </options> |
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154 </param> |
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a018169c73d2
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155 </when> |
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a018169c73d2
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156 </conditional> |
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iuc
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157 </repeat> |
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a018169c73d2
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158 |
|
a018169c73d2
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159 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!"> |
|
a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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160 <conditional name="anywhere_adapter_source"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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161 <param name="anywhere_adapter_source_list" type="select" label="Source"> |
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a018169c73d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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162 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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163 <option value="user">Enter custom sequence</option> |
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164 </param> |
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165 |
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166 <when value="user"> |
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167 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> |
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168 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> |
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169 </when> |
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170 <when value="builtin"> |
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171 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter"> |
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172 <options from_data_table="adapters"> |
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173 <filter type="sort_by" column="1" /> |
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174 </options> |
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175 </param> |
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176 </when> |
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177 </conditional> |
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178 </repeat> |
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179 |
|
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180 <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." /> |
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a018169c73d2
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181 |
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182 </section> |
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183 |
|
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184 </xml> |
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185 |
|
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186 <xml name="paired_end_options" > |
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187 |
|
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188 <!-- Read 1 Options --> |
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189 <expand macro="single_end_options" /> |
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190 |
|
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191 <!-- Read 2 Options --> |
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192 <section name="r2" title="Read 2 Options" expanded="True"> |
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193 |
|
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194 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
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a018169c73d2
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195 <conditional name="adapter_source2"> |
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196 <param name="adapter_source_list2" type="select" label="Source" > |
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197 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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198 <option value="user">Enter custom sequence</option> |
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199 </param> |
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200 |
|
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201 <when value="user"> |
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202 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> |
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203 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> |
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204 </when> |
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205 |
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206 <when value="builtin"> |
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207 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter"> |
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208 <options from_data_table="adapters"> |
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209 <filter type="sort_by" column="1" /> |
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210 </options> |
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211 </param> |
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212 </when> |
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213 </conditional> |
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214 </repeat> |
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215 |
|
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216 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
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a018169c73d2
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217 <conditional name="front_adapter_source2"> |
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218 <param name="front_adapter_source_list2" type="select" label="Source"> |
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219 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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220 <option value="user">Enter custom sequence</option> |
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221 </param> |
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222 |
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223 <when value="user"> |
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224 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> |
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225 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> |
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226 </when> |
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227 <when value="builtin"> |
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228 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter"> |
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229 <options from_data_table="adapters"> |
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230 <filter type="sort_by" column="1" /> |
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231 </options> |
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232 </param> |
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233 </when> |
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234 </conditional> |
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235 </repeat> |
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236 |
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237 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!"> |
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a018169c73d2
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238 <conditional name="anywhere_adapter_source2"> |
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239 <param name="anywhere_adapter_source_list2" type="select" label="Source"> |
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240 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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241 <option value="user">Enter custom sequence</option> |
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a018169c73d2
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242 </param> |
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243 |
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244 <when value="user"> |
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245 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> |
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246 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> |
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247 </when> |
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248 <when value="builtin"> |
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249 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"> |
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250 <options from_data_table="adapters"> |
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251 <filter type="sort_by" column="1" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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252 </options> |
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253 </param> |
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254 </when> |
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255 </conditional> |
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256 </repeat> |
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257 |
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258 <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." /> |
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259 |
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260 </section> |
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261 |
|
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262 </xml> |
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263 |
|
3
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264 <xml name="inherit_format_1"> |
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265 <actions> |
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266 <conditional name="library.type"> |
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267 <when value="single"> |
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268 <action type="format"> |
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269 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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270 </action> |
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271 </when> |
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272 <when value="paired"> |
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273 <action type="format"> |
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274 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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275 </action> |
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276 </when> |
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277 <when value="paired_collection"> |
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278 <action type="format"> |
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279 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
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280 </action> |
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281 </when> |
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282 </conditional> |
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283 </actions> |
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284 </xml> |
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285 |
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286 <xml name="inherit_format_2"> |
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287 <actions> |
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288 <conditional name="library.type"> |
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289 <when value="paired"> |
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290 <action type="format"> |
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291 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
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292 </action> |
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293 </when> |
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294 <when value="paired_collection"> |
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295 <action type="format"> |
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296 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
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297 </action> |
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298 </when> |
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299 </conditional> |
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300 </actions> |
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301 </xml> |
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302 |
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2
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303 </macros> |